I just have one more question, i functionalized Mn-contained nanotube by another O-contained moleculeA new bond formed between Zn and O. If i want to study the whole struture with MD. How should i define this bond in ffbonded.itp
I attach pictures( what quantity for epsilon,LJ parameters, ffbonded.itp?) Sigma would be binding distance?
Basically the LJ parameters are coordinates to the minimum of the potential. So epsilon is the well-depth and sigma the distance value. I guess you must convert the parameters based on what gromacs uses in its files (eV->kcal/mol and A->nm ?)